RetrogeneDB ID: retro_mmul_677

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214344360:143..497(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000005059
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.873
• Ensembl ID: ENSMMUG00000022101
• Aliases: None
• Description: cold-inducible RNA-binding protein [Source:RefSeq peptide;Acc:NP_001248245]

Sequence

>retro_mmul_677
GCAGATCGCCCAGGAAAGGTCTTCGTTGGTGGACTTAGTACGGAAACAAATAAGAAAGCTCTTGAAGCAGTATTTGGCAA
ATATGGACGAATAGTGGAAGCACTCTTGAGGAAAGACCATGAAACCAACAAATCAAGAGGATTTGCTTTTGTCACCTTTG
AAAGCCCAGCAGACGCTAAGGATGCAGCCAGAGACATGAATGGAAAGTCATTAGATGGAAAAGCGATCAAGGTGGAACAA
GCCACCAAACCATCATTTGAAAGTGGTAGACATGGACTGCCTCCACCTCCAAGAAGTAGAGGCCCTCCAAGAGGTCTTAG
AGGTGGAAGAGGAGGAAGTGGAGGAACCAGGGGA

Alignment

ORF - retro_mmul_677 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.55 %
• Parental protein coverage: 59.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKS
          A...GK.FVGGLS..TN...LE.VF.KYG.I.E....KD.ET..SRGF.FVTFE...DAKDA...MNGKS
Retrocopy ADRPGKVFVGGLSTETNKKALEAVFGKYGRIVEALLRKDHETNKSRGFAFVTFESPADAKDAARDMNGKS

Parental  VDGRQIRVDQAGKSSDNRSRGYRGGSAGGRGFFRGGRGRGRGFSRGGGDRG
          .DG..I.V.QA.K.S....R.........RG..RG.RG.GRG.S..GG.RG
Retrocopy LDGKAIKVEQATKPSFESGRHGLPPPPRSRGPPRGLRG-GRGGS--GGTRG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	2.80 RPM	112.83 RPM
SRP007412_brain_prefrontal_cortex	1.90 RPM	121.14 RPM
SRP007412_cerebellum	2.52 RPM	163.83 RPM
SRP007412_heart	1.35 RPM	153.16 RPM
SRP007412_kidney	1.64 RPM	121.36 RPM
SRP007412_liver	0.40 RPM	85.22 RPM
SRP007412_testis	0.53 RPM	184.81 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_677 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_677 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_677 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Gadus morhua	ENSGMOG00000012137	1 retrocopy	retro_gmor_4,
Myotis lucifugus	ENSMLUG00000015007	1 retrocopy	retro_mluc_1975,
Macaca mulatta	ENSMMUG00000022101	4 retrocopies	retro_mmul_1101, retro_mmul_2077, retro_mmul_510, retro_mmul_677 ,
Tursiops truncatus	ENSTTRG00000011049	1 retrocopy	retro_ttru_756,